## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Esp_1_2012-08-22/US_Cal_Esp_1_2012-08-22.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Esp_1_2012-08-22/US_Cal_Esp_1_2012-08-22.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Esp_1_2012-08-22/US_Cal_Esp_1_2012-08-22.mark_duplicates_report.txt REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=SILENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader # Started on: Fri Jan 20 17:25:01 UTC 2023 ## METRICS CLASS picard.sam.DuplicationMetrics LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED SECONDARY_OR_SUPPLEMENTARY_RDS UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE lib1 3397460 36165885 0 0 1346429 2238614 0 0.076901 279954680 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 31665062 31665062 2.0 1.878812 1528387 1528387 3.0 2.651121 73192 73192 4.0 3.329836 7008 7008 5.0 3.926298 2374 2374 6.0 4.450476 1278 1278 7.0 4.91113 787 787 8.0 5.315958 457 457 9.0 5.671725 389 389 10.0 5.984378 278 278 11.0 6.25914 210 210 12.0 6.500605 165 165 13.0 6.712807 147 147 14.0 6.899292 113 113 15.0 7.063178 107 107 16.0 7.207202 89 89 17.0 7.333773 79 79 18.0 7.445004 66 66 19.0 7.542756 68 68 20.0 7.628661 66 66 21.0 7.704155 41 41 22.0 7.770501 42 42 23.0 7.828806 35 35 24.0 7.880045 40 40 25.0 7.925075 39 39 26.0 7.964647 30 30 27.0 7.999424 41 41 28.0 8.029986 24 24 29.0 8.056845 29 29 30.0 8.080448 27 27 31.0 8.101191 24 24 32.0 8.119421 16 16 33.0 8.135441 21 21 34.0 8.149519 32 32 35.0 8.161892 18 18 36.0 8.172765 28 28 37.0 8.18232 12 12 38.0 8.190718 14 14 39.0 8.198097 15 15 40.0 8.204583 13 13 41.0 8.210282 18 18 42.0 8.215291 18 18 43.0 8.219693 9 9 44.0 8.223561 10 10 45.0 8.22696 15 15 46.0 8.229948 15 15 47.0 8.232573 9 9 48.0 8.234881 7 7 49.0 8.236908 7 7 50.0 8.23869 8 8 51.0 8.240256 9 9 52.0 8.241632 8 8 53.0 8.242842 7 7 54.0 8.243905 7 7 55.0 8.244839 13 13 56.0 8.24566 7 7 57.0 8.246381 7 7 58.0 8.247015 8 8 59.0 8.247572 9 9 60.0 8.248062 10 10 61.0 8.248492 7 7 62.0 8.24887 8 8 63.0 8.249202 3 3 64.0 8.249494 5 5 65.0 8.249751 4 4 66.0 8.249977 3 3 67.0 8.250175 7 7 68.0 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